$ perl -Mstrict -Mwarnings -MData::Dumper -E '
open my $inFH, q{<}, \ <<EOF or die $!;
server1,user1,%
server1,user1,db1
server1,user2,%
server1,user3,%
server1,user1,%
server1,user2,%
server1,user2,db2
server1,user3,db3
server1,user3,%
server2,user1,%
server2,user1,db1
server2,user2,%
server2,user3,%
server2,user1,%
server2,user2,%
server2,user2,db2
server2,user3,db3
server2,user3,%
server3,user1,%
server3,user1,db1
server3,user2,%
server3,user3,%
server3,user1,%
server3,user2,%
server3,user2,db2
server3,user3,db3
server3,user3,%
EOF

my @logins = do {
   my %seen;
   map  { [ split m{,} ] }
   grep { ! $seen{ $_ } ++ }
   map  { s{\s*$}{}; $_ }
   <$inFH>;
   };

print Data::Dumper->Dumpxs( [ \ @logins ], [ qw{ *logins } ] );'
@logins = (
            [
              'server1',
              'user1',
              '%'
            ],
            [
              'server1',
              'user1',
              'db1'
            ],
            [
              'server1',
              'user2',
              '%'
            ],
            [
              'server1',
              'user3',
              '%'
            ],
            [
              'server1',
              'user2',
              'db2'
            ],
            [
              'server1',
              'user3',
              'db3'
            ],
            [
              'server2',
              'user1',
              '%'
            ],
            [
              'server2',
              'user1',
              'db1'
            ],
            [
              'server2',
              'user2',
              '%'
            ],
            [
              'server2',
              'user3',
              '%'
            ],
            [
              'server2',
              'user2',
              'db2'
            ],
            [
              'server2',
              'user3',
              'db3'
            ],
            [
              'server3',
              'user1',
              '%'
            ],
            [
              'server3',
              'user1',
              'db1'
            ],
            [
              'server3',
              'user2',
              '%'
            ],
            [
              'server3',
              'user3',
              '%'
            ],
            [
              'server3',
              'user2',
              'db2'
            ],
            [
              'server3',
              'user3',
              'db3'
            ]
          );
$